[gmx-users] polymer NVT

[parinald at unsl.edu.ar]

> Dear Gromacssss
>
>  My system consist of 1 polymer chain, and I need to do NVT simulations,
> so
> I need to fix the box size according to  my polymer density.
>  But I really do not understand editconf?
>
> My edit conf is: ediconf -bt cubic -f file.gro -o out.gro -d 0.5 -center
>
> But in this way I do not get the right density, so I have tried:
>
>
> ediconf -bt cubic -f file.gro -o out.gro -d 0.5 -density 1010
>
> but the resulting  box vector lengths are a=4 b=7 and c=0.3.  Therefore I
> only can use very small cutoffs due to the small c value.
use genbox
>
> And my polymer chain does not look like a Gaussian chain, and it is
> outside
> of the cell.
>
> So, do you have some idea?
>
> .
>
> THANK YOU!!!!
>
> Javier
>
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